The invention discloses a refrigeration power balance control method of a refrigeration container ship and a control system thereof. The method comprises the steps of: collecting the operation states of refrigeration containers, the environment temperature and humidity, the operation states of cargo compartment fans, a wind speed and illuminance; extracting and processing the received information, establishing a nerve network model of the temperature change and energy consumption prediction, and predicting the time and the energy consumption for the refrigeration state of each refrigeration container to reach a critical temperature point; combined with a diesel generator load factor-oil consumption curve and the operation states of the cargo compartment fans, establishing a multi-target power balancing and optimization scheduling module, and solving a control and optimization scheduling strategy of the refrigeration containers; and according to the control and optimization scheduling strategy of the refrigeration containers, sending a control instruction to the refrigeration containers and the cargo compartment fans. According to the invention, the unified scheduling and management of the refrigeration container refrigeration power are realized, the load power balance is maintained, the cargo loading capacity is increased or the installed capacity is lowered, and the ship construction and operation cost is lowered.